Starting phenix.real_space_refine on Sun Jul 5 18:08:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.map" model { file = "/net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zke_14762/07_2026/7zke_14762.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians P 22 5.49 5 Mg 1 5.21 5 S 73 5.16 5 Be 1 3.05 5 C 9225 2.51 5 N 2571 2.21 5 O 2728 1.98 5 F 3 1.80 5 H 14679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29303 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2907 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain: "E" Number of atoms: 25734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1623, 25734 Classifications: {'peptide': 1623} Link IDs: {'PTRANS': 84, 'TRANS': 1538} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.43, per 1000 atoms: 0.15 Number of scatterers: 29303 At special positions: 0 Unit cell: (100.416, 121.336, 149.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 73 16.00 P 22 15.00 Mg 1 11.99 F 3 9.00 O 2728 8.00 N 2571 7.00 C 9225 6.00 Be 1 4.00 H 14679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 857.7 milliseconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 4 sheets defined 68.7% alpha, 5.4% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.818A pdb=" N ILE D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 186 through 194 removed outlier: 3.594A pdb=" N LEU D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 250 removed outlier: 3.711A pdb=" N ILE D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) Proline residue: D 247 - end of helix Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.931A pdb=" N LEU E 12 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 35 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.823A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.562A pdb=" N ARG E 51 " --> pdb=" O PRO E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 72 removed outlier: 3.655A pdb=" N ASN E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 72 " --> pdb=" O ILE E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 116 through 123 removed outlier: 3.546A pdb=" N ILE E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 141 through 157 removed outlier: 4.041A pdb=" N ASN E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 313 through 324 removed outlier: 3.764A pdb=" N VAL E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'E' and resid 348 through 350 No H-bonds generated for 'chain 'E' and resid 348 through 350' Processing helix chain 'E' and resid 357 through 383 removed outlier: 3.538A pdb=" N ARG E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 removed outlier: 4.458A pdb=" N HIS E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 430 removed outlier: 3.807A pdb=" N HIS E 418 " --> pdb=" O VAL E 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 457 removed outlier: 3.599A pdb=" N VAL E 442 " --> pdb=" O ASN E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 removed outlier: 3.934A pdb=" N LEU E 461 " --> pdb=" O ARG E 457 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 457 through 462' Processing helix chain 'E' and resid 464 through 480 removed outlier: 4.244A pdb=" N ILE E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 495 removed outlier: 3.707A pdb=" N LEU E 494 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 495 " --> pdb=" O ALA E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 502 Processing helix chain 'E' and resid 505 through 522 removed outlier: 3.510A pdb=" N LEU E 509 " --> pdb=" O ARG E 505 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU E 520 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN E 522 " --> pdb=" O GLU E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 542 Processing helix chain 'E' and resid 544 through 556 removed outlier: 3.550A pdb=" N LEU E 548 " --> pdb=" O PHE E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 561 Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 568 through 574 Proline residue: E 572 - end of helix Processing helix chain 'E' and resid 578 through 594 Processing helix chain 'E' and resid 596 through 601 removed outlier: 3.594A pdb=" N SER E 600 " --> pdb=" O GLY E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 618 Processing helix chain 'E' and resid 621 through 643 removed outlier: 3.575A pdb=" N ARG E 642 " --> pdb=" O ARG E 638 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP E 643 " --> pdb=" O LEU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 653 removed outlier: 4.726A pdb=" N ALA E 653 " --> pdb=" O ASP E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 663 Processing helix chain 'E' and resid 676 through 680 Processing helix chain 'E' and resid 744 through 766 removed outlier: 3.978A pdb=" N PHE E 765 " --> pdb=" O LEU E 761 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 766 " --> pdb=" O ILE E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 770 Processing helix chain 'E' and resid 771 through 783 removed outlier: 3.812A pdb=" N ALA E 781 " --> pdb=" O ALA E 777 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER E 783 " --> pdb=" O LEU E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 804 Processing helix chain 'E' and resid 806 through 811 removed outlier: 3.842A pdb=" N ALA E 810 " --> pdb=" O THR E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 823 removed outlier: 3.799A pdb=" N ILE E 820 " --> pdb=" O PRO E 816 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 832 through 853 removed outlier: 3.529A pdb=" N VAL E 836 " --> pdb=" O LEU E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 890 Processing helix chain 'E' and resid 890 through 899 Processing helix chain 'E' and resid 903 through 947 Proline residue: E 909 - end of helix removed outlier: 4.858A pdb=" N GLU E 913 " --> pdb=" O PRO E 909 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 968 Processing helix chain 'E' and resid 970 through 992 removed outlier: 3.580A pdb=" N GLN E 986 " --> pdb=" O ALA E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1009 removed outlier: 3.913A pdb=" N ALA E 997 " --> pdb=" O ARG E 993 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS E1009 " --> pdb=" O VAL E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1017 through 1022 removed outlier: 3.700A pdb=" N HIS E1021 " --> pdb=" O GLU E1017 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1033 removed outlier: 3.524A pdb=" N GLN E1032 " --> pdb=" O ILE E1028 " (cutoff:3.500A) Processing helix chain 'E' and resid 1044 through 1072 Processing helix chain 'E' and resid 1074 through 1079 Processing helix chain 'E' and resid 1079 through 1095 removed outlier: 3.862A pdb=" N ARG E1083 " --> pdb=" O VAL E1079 " (cutoff:3.500A) Proline residue: E1089 - end of helix Processing helix chain 'E' and resid 1099 through 1104 Processing helix chain 'E' and resid 1108 through 1124 Processing helix chain 'E' and resid 1128 through 1130 No H-bonds generated for 'chain 'E' and resid 1128 through 1130' Processing helix chain 'E' and resid 1131 through 1147 Proline residue: E1140 - end of helix removed outlier: 3.647A pdb=" N ARG E1147 " --> pdb=" O ILE E1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 1150 through 1168 Processing helix chain 'E' and resid 1168 through 1180 removed outlier: 4.132A pdb=" N THR E1174 " --> pdb=" O VAL E1170 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E1175 " --> pdb=" O ASP E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1181 through 1184 Processing helix chain 'E' and resid 1189 through 1208 removed outlier: 4.115A pdb=" N ARG E1193 " --> pdb=" O ASP E1189 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E1208 " --> pdb=" O ILE E1204 " (cutoff:3.500A) Processing helix chain 'E' and resid 1211 through 1213 No H-bonds generated for 'chain 'E' and resid 1211 through 1213' Processing helix chain 'E' and resid 1214 through 1224 removed outlier: 3.944A pdb=" N VAL E1220 " --> pdb=" O ILE E1216 " (cutoff:3.500A) Proline residue: E1221 - end of helix Processing helix chain 'E' and resid 1230 through 1245 removed outlier: 3.532A pdb=" N THR E1243 " --> pdb=" O THR E1239 " (cutoff:3.500A) Processing helix chain 'E' and resid 1246 through 1251 Proline residue: E1249 - end of helix No H-bonds generated for 'chain 'E' and resid 1246 through 1251' Processing helix chain 'E' and resid 1261 through 1280 removed outlier: 3.522A pdb=" N LEU E1265 " --> pdb=" O SER E1261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E1271 " --> pdb=" O GLY E1267 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR E1273 " --> pdb=" O ASP E1269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE E1274 " --> pdb=" O ARG E1270 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E1280 " --> pdb=" O ALA E1276 " (cutoff:3.500A) Processing helix chain 'E' and resid 1281 through 1284 Processing helix chain 'E' and resid 1298 through 1315 Processing helix chain 'E' and resid 1327 through 1351 removed outlier: 3.610A pdb=" N GLN E1331 " --> pdb=" O GLY E1327 " (cutoff:3.500A) Processing helix chain 'E' and resid 1352 through 1356 Processing helix chain 'E' and resid 1365 through 1367 No H-bonds generated for 'chain 'E' and resid 1365 through 1367' Processing helix chain 'E' and resid 1368 through 1380 Processing helix chain 'E' and resid 1391 through 1398 Processing helix chain 'E' and resid 1400 through 1405 removed outlier: 4.026A pdb=" N ASP E1403 " --> pdb=" O ASP E1400 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E1405 " --> pdb=" O LEU E1402 " (cutoff:3.500A) Processing helix chain 'E' and resid 1412 through 1418 Processing helix chain 'E' and resid 1418 through 1423 Processing helix chain 'E' and resid 1435 through 1439 Processing helix chain 'E' and resid 1443 through 1450 Processing helix chain 'E' and resid 1468 through 1471 Processing helix chain 'E' and resid 1472 through 1480 Processing helix chain 'E' and resid 1486 through 1494 Processing helix chain 'E' and resid 1494 through 1503 removed outlier: 4.245A pdb=" N TYR E1503 " --> pdb=" O ALA E1499 " (cutoff:3.500A) Processing helix chain 'E' and resid 1507 through 1526 Processing helix chain 'E' and resid 1533 through 1538 removed outlier: 4.091A pdb=" N VAL E1537 " --> pdb=" O LEU E1533 " (cutoff:3.500A) Processing helix chain 'E' and resid 1554 through 1568 Processing helix chain 'E' and resid 1568 through 1576 Processing helix chain 'E' and resid 1580 through 1600 Processing helix chain 'E' and resid 1600 through 1605 removed outlier: 4.468A pdb=" N VAL E1604 " --> pdb=" O SER E1600 " (cutoff:3.500A) Processing helix chain 'E' and resid 1611 through 1623 Processing helix chain 'E' and resid 1628 through 1631 Processing helix chain 'E' and resid 1632 through 1645 removed outlier: 3.632A pdb=" N GLY E1636 " --> pdb=" O ALA E1632 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E1639 " --> pdb=" O LEU E1635 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP E1640 " --> pdb=" O GLY E1636 " (cutoff:3.500A) Processing helix chain 'E' and resid 1673 through 1687 removed outlier: 4.020A pdb=" N LEU E1685 " --> pdb=" O GLN E1681 " (cutoff:3.500A) Processing helix chain 'E' and resid 1702 through 1716 removed outlier: 4.226A pdb=" N GLN E1707 " --> pdb=" O ALA E1703 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP E1708 " --> pdb=" O ASN E1704 " (cutoff:3.500A) Processing helix chain 'E' and resid 1726 through 1730 Processing helix chain 'E' and resid 1749 through 1759 removed outlier: 3.653A pdb=" N ASP E1753 " --> pdb=" O ASN E1749 " (cutoff:3.500A) Processing helix chain 'E' and resid 1778 through 1785 removed outlier: 3.763A pdb=" N GLU E1781 " --> pdb=" O GLY E1778 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU E1785 " --> pdb=" O GLU E1782 " (cutoff:3.500A) Processing helix chain 'E' and resid 1786 through 1791 removed outlier: 3.928A pdb=" N PHE E1790 " --> pdb=" O SER E1786 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS E1791 " --> pdb=" O LEU E1787 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1786 through 1791' Processing helix chain 'E' and resid 1856 through 1860 Processing helix chain 'E' and resid 1869 through 1876 removed outlier: 3.509A pdb=" N SER E1875 " --> pdb=" O GLN E1871 " (cutoff:3.500A) Processing helix chain 'E' and resid 1877 through 1884 removed outlier: 3.585A pdb=" N THR E1884 " --> pdb=" O GLY E1880 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 117 through 121 removed outlier: 3.790A pdb=" N GLY D 140 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE D 85 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU D 82 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY D 177 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN D 84 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE D 175 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 86 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE D 175 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY D 231 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 667 through 668 removed outlier: 3.789A pdb=" N VAL E 668 " --> pdb=" O HIS E 671 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 1385 through 1388 removed outlier: 4.684A pdb=" N SER E1411 " --> pdb=" O TYR E1388 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E1361 " --> pdb=" O VAL E1431 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP E1433 " --> pdb=" O LEU E1361 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE E1363 " --> pdb=" O ASP E1433 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS E1430 " --> pdb=" O LEU E1458 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU E1460 " --> pdb=" O CYS E1430 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU E1432 " --> pdb=" O LEU E1460 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY E1318 " --> pdb=" O ARG E1457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E1459 " --> pdb=" O GLY E1318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1544 through 1551 removed outlier: 6.444A pdb=" N ILE E1545 " --> pdb=" O VAL E1771 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ARG E1773 " --> pdb=" O ILE E1545 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN E1547 " --> pdb=" O ARG E1773 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE E1775 " --> pdb=" O GLN E1547 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR E1549 " --> pdb=" O ILE E1775 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL E1741 " --> pdb=" O TYR E1772 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE E1774 " --> pdb=" O VAL E1741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE E1743 " --> pdb=" O ILE E1774 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR E1776 " --> pdb=" O PHE E1743 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU E1668 " --> pdb=" O ILE E1742 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA E1667 " --> pdb=" O LEU E1722 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU E1724 " --> pdb=" O ALA E1667 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE E1669 " --> pdb=" O LEU E1724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU E1695 " --> pdb=" O LEU E1723 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N THR E1725 " --> pdb=" O LEU E1695 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU E1697 " --> pdb=" O THR E1725 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 785 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14657 1.03 - 1.22: 22 1.22 - 1.42: 5999 1.42 - 1.62: 8805 1.62 - 1.81: 128 Bond restraints: 29611 Sorted by residual: bond pdb=" C1' ADP E1902 " pdb=" C2' ADP E1902 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' ADP E1902 " pdb=" O4' ADP E1902 " ideal model delta sigma weight residual 1.426 1.622 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C4 ADP E1902 " pdb=" C5 ADP E1902 " ideal model delta sigma weight residual 1.490 1.329 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C4' ADP E1902 " pdb=" O4' ADP E1902 " ideal model delta sigma weight residual 1.426 1.303 0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C5 ADP E1902 " pdb=" C6 ADP E1902 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.57e+01 ... (remaining 29606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 53607 3.70 - 7.39: 126 7.39 - 11.09: 9 11.09 - 14.78: 1 14.78 - 18.48: 2 Bond angle restraints: 53745 Sorted by residual: angle pdb=" N1 ADP E1902 " pdb=" C6 ADP E1902 " pdb=" N6 ADP E1902 " ideal model delta sigma weight residual 120.00 101.52 18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C5 ADP E1902 " pdb=" C6 ADP E1902 " pdb=" N6 ADP E1902 " ideal model delta sigma weight residual 120.00 138.32 -18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" F2 BEF E1903 " pdb="BE BEF E1903 " pdb=" F3 BEF E1903 " ideal model delta sigma weight residual 119.96 107.32 12.64 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O2B ADP E1902 " pdb=" PB ADP E1902 " pdb=" O3B ADP E1902 " ideal model delta sigma weight residual 119.90 109.05 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1A ADP E1902 " pdb=" PA ADP E1902 " pdb=" O2A ADP E1902 " ideal model delta sigma weight residual 119.90 109.81 10.09 3.00e+00 1.11e-01 1.13e+01 ... (remaining 53740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 12541 19.50 - 38.99: 861 38.99 - 58.49: 249 58.49 - 77.99: 36 77.99 - 97.48: 11 Dihedral angle restraints: 13698 sinusoidal: 7759 harmonic: 5939 Sorted by residual: dihedral pdb=" O1B ADP E1902 " pdb=" O3A ADP E1902 " pdb=" PB ADP E1902 " pdb=" PA ADP E1902 " ideal model delta sinusoidal sigma weight residual -60.00 -157.49 97.48 1 2.00e+01 2.50e-03 2.71e+01 dihedral pdb=" CA ALA E1667 " pdb=" C ALA E1667 " pdb=" N LEU E1668 " pdb=" CA LEU E1668 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP D 96 " pdb=" C ASP D 96 " pdb=" N LEU D 97 " pdb=" CA LEU D 97 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 13695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1509 0.035 - 0.070: 579 0.070 - 0.106: 145 0.106 - 0.141: 87 0.141 - 0.176: 17 Chirality restraints: 2337 Sorted by residual: chirality pdb=" CA THR E1124 " pdb=" N THR E1124 " pdb=" C THR E1124 " pdb=" CB THR E1124 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" C3' DC A 9 " pdb=" C4' DC A 9 " pdb=" O3' DC A 9 " pdb=" C2' DC A 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA ILE E 766 " pdb=" N ILE E 766 " pdb=" C ILE E 766 " pdb=" CB ILE E 766 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 2334 not shown) Planarity restraints: 4246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 567 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO E 568 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 568 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 568 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E1132 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E1133 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E1133 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E1133 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 815 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 816 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 816 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 816 " -0.025 5.00e-02 4.00e+02 ... (remaining 4243 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 2563 2.24 - 2.83: 65257 2.83 - 3.42: 77746 3.42 - 4.01: 103969 4.01 - 4.60: 162492 Nonbonded interactions: 412027 Sorted by model distance: nonbonded pdb=" OE1 GLU E 619 " pdb=" H GLU E 619 " model vdw 1.644 2.450 nonbonded pdb="HH11 ARG D 105 " pdb=" OH TYR E1872 " model vdw 1.661 2.450 nonbonded pdb=" HE ARG E1395 " pdb=" OD2 ASP E1418 " model vdw 1.666 2.450 nonbonded pdb=" OE1 GLU E1017 " pdb=" H GLU E1017 " model vdw 1.671 2.450 nonbonded pdb=" O ASN D 90 " pdb=" HG1 THR D 168 " model vdw 1.682 2.450 ... (remaining 412022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 30.320 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.222 14932 Z= 0.312 Angle : 0.795 18.475 20293 Z= 0.428 Chirality : 0.045 0.176 2337 Planarity : 0.005 0.051 2535 Dihedral : 13.108 97.485 5692 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.26 % Allowed : 2.92 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1783 helix: 0.52 (0.16), residues: 997 sheet: -0.89 (0.43), residues: 114 loop : 0.36 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E1595 TYR 0.016 0.002 TYR E1155 PHE 0.015 0.002 PHE E1192 TRP 0.014 0.002 TRP E 55 HIS 0.007 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.31 (14932) covalent geometry : angle 0.79498 / 0.43 (20293) hydrogen bonds : bond 0.14576 / 13.86 ( 812) hydrogen bonds : angle 5.99887 / 5.40 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 383 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 379 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 439 MET cc_start: 0.6073 (ttm) cc_final: 0.5531 (tpp) REVERT: E 493 THR cc_start: 0.5454 (m) cc_final: 0.5232 (m) REVERT: E 827 SER cc_start: 0.8011 (p) cc_final: 0.7755 (t) REVERT: E 1066 ILE cc_start: 0.8284 (mt) cc_final: 0.8030 (mt) REVERT: E 1491 LEU cc_start: 0.7548 (mt) cc_final: 0.6950 (tp) REVERT: E 1549 TYR cc_start: 0.6198 (t80) cc_final: 0.5755 (t80) REVERT: E 1707 GLN cc_start: 0.7951 (tp40) cc_final: 0.7708 (tp40) outliers start: 4 outliers final: 0 residues processed: 381 average time/residue: 0.2676 time to fit residues: 147.3890 Evaluate side-chains 214 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 803 ASN E 910 GLN E1032 GLN E1277 GLN E1599 ASN ** E1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109111 restraints weight = 63640.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111945 restraints weight = 45033.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113285 restraints weight = 29174.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114024 restraints weight = 22430.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114268 restraints weight = 21160.271| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14932 Z= 0.169 Angle : 0.639 7.672 20293 Z= 0.339 Chirality : 0.041 0.218 2337 Planarity : 0.005 0.048 2535 Dihedral : 10.019 69.431 2157 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.97 % Allowed : 10.05 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1783 helix: 0.97 (0.16), residues: 1006 sheet: -1.14 (0.42), residues: 119 loop : 0.26 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 894 TYR 0.014 0.001 TYR E1155 PHE 0.014 0.001 PHE E 501 TRP 0.026 0.002 TRP E1859 HIS 0.006 0.001 HIS E1761 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (14932) covalent geometry : angle 0.63866 / 0.34 (20293) hydrogen bonds : bond 0.05317 / 4.80 ( 812) hydrogen bonds : angle 4.94837 / 4.57 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 TYR cc_start: 0.7411 (t80) cc_final: 0.7152 (t80) REVERT: E 827 SER cc_start: 0.8550 (p) cc_final: 0.8258 (t) REVERT: E 886 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8397 (tptp) REVERT: E 1136 MET cc_start: 0.8415 (tpp) cc_final: 0.8090 (tpp) REVERT: E 1347 PHE cc_start: 0.7197 (t80) cc_final: 0.6882 (t80) REVERT: E 1676 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7345 (tpt) REVERT: E 1707 GLN cc_start: 0.8341 (tp40) cc_final: 0.7928 (tp40) REVERT: E 1710 VAL cc_start: 0.8357 (p) cc_final: 0.8148 (p) outliers start: 15 outliers final: 6 residues processed: 227 average time/residue: 0.2622 time to fit residues: 90.7220 Evaluate side-chains 212 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 205 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 1269 ASP Chi-restraints excluded: chain E residue 1525 VAL Chi-restraints excluded: chain E residue 1668 LEU Chi-restraints excluded: chain E residue 1676 MET Chi-restraints excluded: chain E residue 1723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 33 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 664 HIS E1277 GLN E1317 HIS ** E1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.151134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105575 restraints weight = 63971.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108162 restraints weight = 46851.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109291 restraints weight = 32444.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111905 restraints weight = 25022.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111990 restraints weight = 20616.711| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 14932 Z= 0.260 Angle : 0.693 9.933 20293 Z= 0.370 Chirality : 0.043 0.165 2337 Planarity : 0.005 0.051 2535 Dihedral : 9.922 71.699 2157 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.23 % Allowed : 10.69 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1783 helix: 0.91 (0.16), residues: 1012 sheet: -1.28 (0.43), residues: 113 loop : -0.13 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 332 TYR 0.019 0.002 TYR E1155 PHE 0.023 0.002 PHE E 501 TRP 0.015 0.002 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (14932) covalent geometry : angle 0.69290 / 0.37 (20293) hydrogen bonds : bond 0.05392 / 4.99 ( 812) hydrogen bonds : angle 4.92682 / 4.66 ( 2310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 318 GLU cc_start: 0.7920 (tp30) cc_final: 0.7709 (mm-30) REVERT: E 627 MET cc_start: 0.7898 (tpp) cc_final: 0.7542 (tpt) REVERT: E 827 SER cc_start: 0.8692 (p) cc_final: 0.8427 (t) REVERT: E 886 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8457 (tptp) REVERT: E 1347 PHE cc_start: 0.7601 (t80) cc_final: 0.7385 (t80) REVERT: E 1708 ASP cc_start: 0.7905 (t0) cc_final: 0.7608 (m-30) outliers start: 19 outliers final: 12 residues processed: 228 average time/residue: 0.2471 time to fit residues: 85.9385 Evaluate side-chains 200 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1668 LEU Chi-restraints excluded: chain E residue 1676 MET Chi-restraints excluded: chain E residue 1769 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 94 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 127 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1277 GLN E1511 GLN E1665 HIS E1746 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105682 restraints weight = 63228.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108777 restraints weight = 46576.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109882 restraints weight = 30865.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112805 restraints weight = 24093.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113104 restraints weight = 19460.627| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14932 Z= 0.174 Angle : 0.595 7.251 20293 Z= 0.314 Chirality : 0.040 0.167 2337 Planarity : 0.005 0.041 2535 Dihedral : 9.832 70.901 2157 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.23 % Allowed : 12.05 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1783 helix: 1.23 (0.16), residues: 1015 sheet: -1.18 (0.44), residues: 113 loop : -0.12 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1759 TYR 0.016 0.001 TYR E1155 PHE 0.021 0.001 PHE E 501 TRP 0.015 0.002 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (14932) covalent geometry : angle 0.59548 / 0.31 (20293) hydrogen bonds : bond 0.04572 / 4.19 ( 812) hydrogen bonds : angle 4.63884 / 4.40 ( 2310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 318 GLU cc_start: 0.7850 (tp30) cc_final: 0.7305 (mm-30) REVERT: E 627 MET cc_start: 0.7961 (tpp) cc_final: 0.7697 (tpp) REVERT: E 827 SER cc_start: 0.8728 (p) cc_final: 0.8439 (t) REVERT: E 886 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8451 (tptp) REVERT: E 1136 MET cc_start: 0.8411 (tpp) cc_final: 0.8104 (tpp) REVERT: E 1156 MET cc_start: 0.7351 (mmm) cc_final: 0.7018 (mmm) REVERT: E 1347 PHE cc_start: 0.7724 (t80) cc_final: 0.7513 (t80) REVERT: E 1707 GLN cc_start: 0.8453 (tp40) cc_final: 0.7843 (tp40) outliers start: 19 outliers final: 11 residues processed: 195 average time/residue: 0.2383 time to fit residues: 71.5358 Evaluate side-chains 185 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 921 VAL Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1339 ASP Chi-restraints excluded: chain E residue 1710 VAL Chi-restraints excluded: chain E residue 1769 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 146 optimal weight: 0.0670 chunk 127 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1277 GLN E1665 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.152642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107082 restraints weight = 63275.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110016 restraints weight = 45187.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110977 restraints weight = 27935.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114511 restraints weight = 23889.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114340 restraints weight = 18599.509| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14932 Z= 0.119 Angle : 0.544 6.639 20293 Z= 0.284 Chirality : 0.038 0.142 2337 Planarity : 0.004 0.080 2535 Dihedral : 9.715 71.751 2157 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.91 % Allowed : 12.90 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1783 helix: 1.52 (0.16), residues: 1016 sheet: -1.06 (0.45), residues: 113 loop : -0.07 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1759 TYR 0.013 0.001 TYR E1155 PHE 0.019 0.001 PHE E1713 TRP 0.019 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (14932) covalent geometry : angle 0.54440 / 0.28 (20293) hydrogen bonds : bond 0.04096 / 3.75 ( 812) hydrogen bonds : angle 4.39151 / 4.11 ( 2310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 TRP cc_start: 0.8056 (t-100) cc_final: 0.7696 (t-100) REVERT: E 318 GLU cc_start: 0.7783 (tp30) cc_final: 0.7224 (mm-30) REVERT: E 627 MET cc_start: 0.7950 (tpp) cc_final: 0.7739 (tpp) REVERT: E 827 SER cc_start: 0.8666 (p) cc_final: 0.8379 (t) REVERT: E 886 LYS cc_start: 0.8686 (tmtt) cc_final: 0.8430 (tptp) REVERT: E 917 GLN cc_start: 0.8120 (mt0) cc_final: 0.7743 (mt0) REVERT: E 1136 MET cc_start: 0.8294 (tpp) cc_final: 0.8033 (tpp) REVERT: E 1156 MET cc_start: 0.7346 (mmm) cc_final: 0.7061 (mmm) REVERT: E 1347 PHE cc_start: 0.7713 (t80) cc_final: 0.7487 (t80) REVERT: E 1480 MET cc_start: 0.8372 (mtp) cc_final: 0.8123 (mtp) REVERT: E 1707 GLN cc_start: 0.8449 (tp40) cc_final: 0.7823 (tp40) outliers start: 14 outliers final: 11 residues processed: 197 average time/residue: 0.2351 time to fit residues: 71.8172 Evaluate side-chains 190 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1710 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 144 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1277 GLN E1599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106745 restraints weight = 62929.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110154 restraints weight = 45379.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111213 restraints weight = 30005.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113856 restraints weight = 23228.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114126 restraints weight = 19355.813| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14932 Z= 0.127 Angle : 0.542 7.305 20293 Z= 0.283 Chirality : 0.038 0.172 2337 Planarity : 0.004 0.064 2535 Dihedral : 9.648 70.849 2157 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.04 % Allowed : 12.90 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1783 helix: 1.64 (0.17), residues: 1020 sheet: -0.93 (0.46), residues: 113 loop : -0.02 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 505 TYR 0.013 0.001 TYR E1155 PHE 0.022 0.001 PHE E1713 TRP 0.016 0.001 TRP E1859 HIS 0.005 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14932) covalent geometry : angle 0.54195 / 0.28 (20293) hydrogen bonds : bond 0.03899 / 3.58 ( 812) hydrogen bonds : angle 4.30454 / 4.03 ( 2310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 TRP cc_start: 0.8094 (t-100) cc_final: 0.7775 (t-100) REVERT: E 140 LEU cc_start: 0.7421 (tp) cc_final: 0.6745 (tp) REVERT: E 318 GLU cc_start: 0.7843 (tp30) cc_final: 0.7270 (mm-30) REVERT: E 627 MET cc_start: 0.8008 (tpp) cc_final: 0.7461 (tpp) REVERT: E 886 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8413 (tptp) REVERT: E 910 GLN cc_start: 0.6232 (pm20) cc_final: 0.5970 (pm20) REVERT: E 917 GLN cc_start: 0.8116 (mt0) cc_final: 0.7769 (mt0) REVERT: E 1136 MET cc_start: 0.8286 (tpp) cc_final: 0.8046 (tpp) REVERT: E 1156 MET cc_start: 0.7402 (mmm) cc_final: 0.7141 (mmm) REVERT: E 1347 PHE cc_start: 0.7804 (t80) cc_final: 0.7591 (t80) REVERT: E 1480 MET cc_start: 0.8333 (mtp) cc_final: 0.8089 (mtp) REVERT: E 1511 GLN cc_start: 0.4743 (mm-40) cc_final: 0.4490 (mm-40) REVERT: E 1522 HIS cc_start: 0.7186 (t-90) cc_final: 0.6475 (m170) REVERT: E 1707 GLN cc_start: 0.8411 (tp40) cc_final: 0.7752 (tp40) outliers start: 16 outliers final: 14 residues processed: 198 average time/residue: 0.2647 time to fit residues: 77.9815 Evaluate side-chains 189 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1735 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 146 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1277 GLN E1599 ASN E1746 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106267 restraints weight = 61943.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108231 restraints weight = 33941.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109045 restraints weight = 26746.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110132 restraints weight = 21462.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110300 restraints weight = 19413.435| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14932 Z= 0.139 Angle : 0.550 6.668 20293 Z= 0.286 Chirality : 0.039 0.154 2337 Planarity : 0.004 0.060 2535 Dihedral : 9.583 70.349 2157 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.04 % Allowed : 13.22 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1783 helix: 1.69 (0.17), residues: 1020 sheet: -0.85 (0.47), residues: 111 loop : -0.08 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1639 TYR 0.015 0.001 TYR E1155 PHE 0.026 0.001 PHE E1713 TRP 0.019 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14932) covalent geometry : angle 0.54993 / 0.29 (20293) hydrogen bonds : bond 0.03873 / 3.57 ( 812) hydrogen bonds : angle 4.27924 / 4.02 ( 2310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 318 GLU cc_start: 0.7868 (tp30) cc_final: 0.7400 (mm-30) REVERT: E 627 MET cc_start: 0.8026 (tpp) cc_final: 0.7538 (tpp) REVERT: E 910 GLN cc_start: 0.6346 (pm20) cc_final: 0.6094 (pm20) REVERT: E 917 GLN cc_start: 0.7918 (mt0) cc_final: 0.7581 (mt0) REVERT: E 1136 MET cc_start: 0.8263 (tpp) cc_final: 0.7778 (mmm) REVERT: E 1156 MET cc_start: 0.7452 (mmm) cc_final: 0.7217 (mmm) REVERT: E 1347 PHE cc_start: 0.7699 (t80) cc_final: 0.7499 (t80) REVERT: E 1480 MET cc_start: 0.8359 (mtp) cc_final: 0.8080 (mtp) REVERT: E 1522 HIS cc_start: 0.7173 (t-90) cc_final: 0.6459 (m170) outliers start: 16 outliers final: 14 residues processed: 187 average time/residue: 0.2236 time to fit residues: 65.3399 Evaluate side-chains 179 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1735 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1277 GLN E1746 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.149805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103649 restraints weight = 62911.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107992 restraints weight = 44529.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108964 restraints weight = 27438.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111289 restraints weight = 21985.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111435 restraints weight = 18840.436| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14932 Z= 0.172 Angle : 0.564 8.426 20293 Z= 0.296 Chirality : 0.039 0.152 2337 Planarity : 0.004 0.066 2535 Dihedral : 9.567 69.027 2157 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.17 % Allowed : 13.67 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1783 helix: 1.69 (0.16), residues: 1025 sheet: -0.79 (0.46), residues: 117 loop : -0.12 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 904 TYR 0.052 0.002 TYR E1300 PHE 0.016 0.001 PHE D 242 TRP 0.020 0.002 TRP E1859 HIS 0.007 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (14932) covalent geometry : angle 0.56395 / 0.30 (20293) hydrogen bonds : bond 0.04014 / 3.71 ( 812) hydrogen bonds : angle 4.30086 / 4.05 ( 2310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 627 MET cc_start: 0.8044 (tpp) cc_final: 0.7620 (tpp) REVERT: E 910 GLN cc_start: 0.6237 (pm20) cc_final: 0.5943 (pm20) REVERT: E 917 GLN cc_start: 0.8105 (mt0) cc_final: 0.7753 (mt0) REVERT: E 1136 MET cc_start: 0.8285 (tpp) cc_final: 0.7794 (mmm) REVERT: E 1156 MET cc_start: 0.7616 (mmm) cc_final: 0.7404 (mmm) REVERT: E 1522 HIS cc_start: 0.7206 (t-90) cc_final: 0.6583 (m170) outliers start: 18 outliers final: 17 residues processed: 191 average time/residue: 0.2462 time to fit residues: 71.8502 Evaluate side-chains 189 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1735 LEU Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 116 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1277 GLN E1511 GLN E1746 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114651 restraints weight = 59674.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113376 restraints weight = 40235.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114805 restraints weight = 45047.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115637 restraints weight = 30981.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116017 restraints weight = 27522.764| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14932 Z= 0.115 Angle : 0.546 7.825 20293 Z= 0.280 Chirality : 0.038 0.143 2337 Planarity : 0.004 0.062 2535 Dihedral : 9.505 69.159 2157 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.30 % Allowed : 14.13 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1783 helix: 1.85 (0.17), residues: 1024 sheet: -0.61 (0.48), residues: 112 loop : 0.05 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 111 TYR 0.025 0.001 TYR E1300 PHE 0.014 0.001 PHE D 242 TRP 0.021 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14932) covalent geometry : angle 0.54569 / 0.28 (20293) hydrogen bonds : bond 0.03677 / 3.39 ( 812) hydrogen bonds : angle 4.15953 / 3.90 ( 2310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 627 MET cc_start: 0.7876 (tpp) cc_final: 0.7560 (tpp) REVERT: E 910 GLN cc_start: 0.6543 (pm20) cc_final: 0.6265 (pm20) REVERT: E 917 GLN cc_start: 0.8013 (mt0) cc_final: 0.7712 (mt0) REVERT: E 1049 GLU cc_start: 0.7688 (tp30) cc_final: 0.7462 (tp30) REVERT: E 1136 MET cc_start: 0.8184 (tpp) cc_final: 0.7723 (mmm) REVERT: E 1522 HIS cc_start: 0.7172 (t-90) cc_final: 0.6818 (m170) outliers start: 20 outliers final: 16 residues processed: 185 average time/residue: 0.2362 time to fit residues: 67.8449 Evaluate side-chains 186 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1511 GLN Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 0.0470 chunk 85 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 522 ASN E1277 GLN E1746 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111056 restraints weight = 59635.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114641 restraints weight = 54369.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116126 restraints weight = 33982.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116358 restraints weight = 26094.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116738 restraints weight = 24002.904| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14932 Z= 0.142 Angle : 0.553 7.928 20293 Z= 0.286 Chirality : 0.039 0.161 2337 Planarity : 0.004 0.042 2535 Dihedral : 9.491 68.607 2157 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.10 % Allowed : 14.26 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.21), residues: 1783 helix: 1.80 (0.17), residues: 1030 sheet: -0.61 (0.48), residues: 112 loop : 0.00 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 505 TYR 0.032 0.001 TYR E1300 PHE 0.014 0.001 PHE D 242 TRP 0.019 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14932) covalent geometry : angle 0.55348 / 0.29 (20293) hydrogen bonds : bond 0.03730 / 3.45 ( 812) hydrogen bonds : angle 4.17503 / 3.92 ( 2310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 627 MET cc_start: 0.7919 (tpp) cc_final: 0.7596 (tpp) REVERT: E 910 GLN cc_start: 0.6474 (pm20) cc_final: 0.6190 (pm20) REVERT: E 917 GLN cc_start: 0.8024 (mt0) cc_final: 0.7724 (mt0) REVERT: E 1049 GLU cc_start: 0.7754 (tp30) cc_final: 0.7509 (tp30) REVERT: E 1136 MET cc_start: 0.8242 (tpp) cc_final: 0.7755 (mmm) REVERT: E 1303 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6897 (tp30) REVERT: E 1522 HIS cc_start: 0.7152 (t-90) cc_final: 0.6771 (m-70) outliers start: 17 outliers final: 15 residues processed: 188 average time/residue: 0.2554 time to fit residues: 74.8813 Evaluate side-chains 189 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 175 optimal weight: 0.0030 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111462 restraints weight = 59999.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115435 restraints weight = 60517.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116534 restraints weight = 36269.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117159 restraints weight = 29135.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117499 restraints weight = 27193.465| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14932 Z= 0.143 Angle : 0.557 8.297 20293 Z= 0.288 Chirality : 0.039 0.147 2337 Planarity : 0.004 0.041 2535 Dihedral : 9.441 67.698 2157 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.17 % Allowed : 14.13 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1783 helix: 1.79 (0.16), residues: 1036 sheet: -0.60 (0.48), residues: 112 loop : -0.01 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 111 TYR 0.034 0.001 TYR E1300 PHE 0.016 0.001 PHE E1713 TRP 0.024 0.001 TRP E1859 HIS 0.007 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14932) covalent geometry : angle 0.55719 / 0.29 (20293) hydrogen bonds : bond 0.03746 / 3.49 ( 812) hydrogen bonds : angle 4.14574 / 3.90 ( 2310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.35 seconds wall clock time: 67 minutes 21.73 seconds (4041.73 seconds total)